[gmx-users] number of water molecules affects the PMF
x.periole at rug.nl
Wed Jun 2 09:58:04 CEST 2010
On Jun 2, 2010, at 9:49 AM, Ozge Engin wrote:
> Hi Chris,
> The two setups were different from each other in terms of only the
> number of water molecules. Even the starting
> conformations for the two peptides were the same. I especially took
> care about that to leave only the number of molecules as a variable.
> I calculated the error by dividing the whole data to 4, and
> calculated the standard deviation between the 4 sets, and divided
> the result by sqrt (3).
> For the Xavier's suggestion: I think I should wait a little, at
> least until having the same length of trajectory for the two sets.
Here we go! You are probably not converged! How long did you simulate?
> Ozge Engin
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